SMED30018840

Overview
NameSMED30018840
Smed IDSMED30018840
Length (bp)1297
Neoblast Clusters

Zeng et. al., 2018



▻ Overview

▻ Neoblast Population

 

 

Overview

 

Single cell RNA-seq of pluripotent neoblasts and its early progenies


We isolated X1 neoblasts cells enriched in high piwi-1 expression (Neoblast Population), and profiled ∼7,614 individual cells via scRNA-seq. Unsupervised analyses uncovered 12 distinct classes from 7,088 high-quality cells. We designated these classes Nb1 to Nb12 and ordered them based on high (Nb1) to low (Nb12) piwi-1 expression levels. We further defined groups of genes that best classified the cells parsed into 12 distinct cell clusters to generate a scaled expression heat map of discriminative gene sets for each cluster. Expression of each cluster’s gene signatures was validated using multiplex fluorescence in situ hybridization (FISH) co-stained with piwi-1 and largely confirmed the cell clusters revealed by scRNA-seq.

We also tested sub-lethal irradiation exposure. To profile rare pluripotent stem cells (PSCs) and avoid interference from immediate progenitor cells, we determined a time point after sub-lethal irradiation (7 DPI) with minimal piwi-1+ cells, followed by isolation and single-cell RNA-seq of 1,200 individual cells derived from X1 (Piwi-1 high) and X2 (Piwi-1 low) cell populations (Sub-lethal Irradiated Surviving X1 and X2 Cell Population)



Explore this single cell expression dataset with our NB Cluster Shiny App



 

Neoblast Population

 

t-SNE plot shows two-dimensional representation of global gene expression relationships among all neoblasts (n = 7,088 after filter). Cluster identity was assigned based on the top 10 marker genes of each cluster (Table S2), followed by inspection of RNA in situ hybridization patterns. Neoblast groups, Nb.


Expression of SMED30018840 (SMED30018840) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30018840 (SMED30018840) in cells (dots) of each of the 12 neoblast clusters.

 

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Embryonic Expression

Davies et. al., 2017

Hover the mouse over a column in the graph to view average RPKM values per sample.
Sort Descending | Sort Ascending | Only Non-Zero Values | Tile/Chart | Reset

Embryonic Stages: Y: yolk. S2-S8: Stages 2-8. C4: asexual adult. SX: virgin, sexually mature adult.
For further information about sample preparation and analysis for the single animal RNA-Seq experiment, please refer to the Materials and Methods

 

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Anatomical Expression

PAGE et. al., 2020



SMED30018840

has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGE



PAGE Curations: 1

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
parenchymaSMED30018840SMESG000058813.1 dd_Smed_v4_74877_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30018840 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.003875:7734..12874 -6279
Homology
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BLAST of SMED30018840 vs. Planmine SMEST
Match: SMESG000058813.1 (SMESG000058813.1)

HSP 1 Score: 379.793 bits (974), Expect = 7.185e-180
Identity = 187/187 (100.00%), Postives = 187/187 (100.00%), Query Frame = 1 
Query:   34 MTYDKNQFQATVLLNDALNVLYEASLTYQNNHLTGKEIFRISFKFFEERCDFDINKIAISNFCQFLLNSNKIYTESSNASDKTNFKKSKKVTYKMFEMNDNVNYIKKSFQHKIMSSINDGITFLRKKIGLGTKYIMCHERKFCLIHLLKIIDLSHIENLIYLVDLSKDCEHEFDNISGEFQTKFHTQ 594
            MTYDKNQFQATVLLNDALNVLYEASLTYQNNHLTGKEIFRISFKFFEERCDFDINKIAISNFCQFLLNSNKIYTESSNASDKTNFKKSKKVTYKMFEMNDNVNYIKKSFQHKIMSSINDGITFLRKKIGLGTKYIMCHERKFCLIHLLKIIDLSHIENLIYLVDLSKDCEHEFDNISGEFQTKFHTQ
Sbjct:    1 MTYDKNQFQATVLLNDALNVLYEASLTYQNNHLTGKEIFRISFKFFEERCDFDINKIAISNFCQFLLNSNKIYTESSNASDKTNFKKSKKVTYKMFEMNDNVNYIKKSFQHKIMSSINDGITFLRKKIGLGTKYIMCHERKFCLIHLLKIIDLSHIENLIYLVDLSKDCEHEFDNISGEFQTKFHTQ 187

HSP 2 Score: 270.781 bits (691), Expect = 7.185e-180
Identity = 144/199 (72.36%), Postives = 145/199 (72.86%), Query Frame = 2 
Query:  635 FFNRKEMNTLPLYNIHWDCIFYKLKGKINKIPQNVLSNLKDEYLNTIKTFIERPDLLKWNYLTQVFTLLPKLIKQNKKHLVIKILQLCFHLLPKKSFYLSEHLVLGLSNLFSAKSYEQKLYNKFAKLFNFDFKNQNYKTSLINFILKNSVYLFRFPSEIIQETTNMKLAIADFETLTVGKADFKEYEILTSEVTAKAIC 1231
            F  +KEMNTLPLYNIHWDCIFYKLKGKINKIPQNVLSNLKDEYLNTIKTFIERPDLLKWNYLTQ                                                    EQKLYNKFAKLFNFDFKNQNYKTSLINFILKNSVYLFRFPSEIIQETTNMKLAIADFETLTVGKADFKEYEILTSEVTAKAIC
Sbjct:  184 FHTQKEMNTLPLYNIHWDCIFYKLKGKINKIPQNVLSNLKDEYLNTIKTFIERPDLLKWNYLTQ----------------------------------------------------EQKLYNKFAKLFNFDFKNQNYKTSLINFILKNSVYLFRFPSEIIQETTNMKLAIADFETLTVGKADFKEYEILTSEVTAKAIC 330
[Close]
BLAST of SMED30018840 vs. Planmine SMEST
Match: SMESG000058813.1 (SMESG000058813.1)

HSP 1 Score: 379.793 bits (974), Expect = 1.930e-138
Identity = 187/187 (100.00%), Postives = 187/187 (100.00%), Query Frame = 1 
Query:   34 MTYDKNQFQATVLLNDALNVLYEASLTYQNNHLTGKEIFRISFKFFEERCDFDINKIAISNFCQFLLNSNKIYTESSNASDKTNFKKSKKVTYKMFEMNDNVNYIKKSFQHKIMSSINDGITFLRKKIGLGTKYIMCHERKFCLIHLLKIIDLSHIENLIYLVDLSKDCEHEFDNISGEFQTKFHTQ 594
            MTYDKNQFQATVLLNDALNVLYEASLTYQNNHLTGKEIFRISFKFFEERCDFDINKIAISNFCQFLLNSNKIYTESSNASDKTNFKKSKKVTYKMFEMNDNVNYIKKSFQHKIMSSINDGITFLRKKIGLGTKYIMCHERKFCLIHLLKIIDLSHIENLIYLVDLSKDCEHEFDNISGEFQTKFHTQ
Sbjct:    1 MTYDKNQFQATVLLNDALNVLYEASLTYQNNHLTGKEIFRISFKFFEERCDFDINKIAISNFCQFLLNSNKIYTESSNASDKTNFKKSKKVTYKMFEMNDNVNYIKKSFQHKIMSSINDGITFLRKKIGLGTKYIMCHERKFCLIHLLKIIDLSHIENLIYLVDLSKDCEHEFDNISGEFQTKFHTQ 187

HSP 2 Score: 132.88 bits (333), Expect = 1.930e-138
Identity = 61/64 (95.31%), Postives = 62/64 (96.88%), Query Frame = 2 
Query:  635 FFNRKEMNTLPLYNIHWDCIFYKLKGKINKIPQNVLSNLKDEYLNTIKTFIERPDLLKWNYLTQ 826
            F  +KEMNTLPLYNIHWDCIFYKLKGKINKIPQNVLSNLKDEYLNTIKTFIERPDLLKWNYLTQ
Sbjct:  184 FHTQKEMNTLPLYNIHWDCIFYKLKGKINKIPQNVLSNLKDEYLNTIKTFIERPDLLKWNYLTQ 247

HSP 3 Score: 111.309 bits (277), Expect = 3.636e-27
Identity = 53/57 (92.98%), Postives = 56/57 (98.25%), Query Frame = 2 
Query: 1061 NFILKNSVYLFRFPSEIIQETTNMKLAIADFETLTVGKADFKEYEILTSEVTAKAIC 1231
            N++ +NSVYLFRFPSEIIQETTNMKLAIADFETLTVGKADFKEYEILTSEVTAKAIC
Sbjct:  243 NYLTQNSVYLFRFPSEIIQETTNMKLAIADFETLTVGKADFKEYEILTSEVTAKAIC 299
The following BLAST results are available for this feature:
BLAST of SMED30018840 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30018840 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30018840 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30018840 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30018840 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30018840 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30018840 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30018840 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30018840 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30018840 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30018840 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30018840 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30018840 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30018840 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 2
Match NameE-valueIdentityDescription
SMESG000058813.17.185e-180100.00SMESG000058813.1[more]
SMESG000058813.11.930e-138100.00SMESG000058813.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30018840 ID=SMED30018840|Name=SMED30018840|organism=Schmidtea mediterranea sexual|type=transcript|length=1297bp
TAATAATTATCTTTTTAAGTTTATTTTAAGCAAATGACTTATGATAAAAA
TCAATTTCAAGCTACAGTTTTATTAAATGATGCTCTGAATGTTTTGTATG
AAGCTTCGCTGACATATCAAAATAACCACCTTACAGGCAAAGAAATATTT
AGAATATCTTTCAAATTTTTTGAAGAAAGGTGTGATTTTGACATCAATAA
AATAGCAATCAGTAACTTTTGTCAGTTTCTTTTGAATTCAAATAAAATCT
ACACTGAATCATCTAATGCTTCCGACAAGACTAATTTCAAAAAATCAAAA
AAAGTTACCTACAAGATGTTTGAAATGAATGATAATGTAAATTATATCAA
AAAGTCTTTCCAACATAAAATAATGTCATCAATTAATGATGGCATAACAT
TTTTGAGGAAAAAAATCGGATTGGGAACTAAATATATAATGTGTCACGAG
CGAAAGTTTTGTTTAATTCATCTTCTTAAAATAATAGATTTATCACATAT
TGAAAATCTAATTTATCTCGTTGATTTGAGTAAAGATTGTGAACACGAGT
TTGATAATATATCTGGGGAATTTCAAACCAAATTCCACACACAGTAATTT
TGTTTGTCAAACTCGTTCTACTTTGTAATTTTATTTTTTTAATAGAAAAG
AAATGAATACCCTACCATTGTATAATATTCATTGGGATTGTATATTTTAC
AAATTAAAAGGAAAAATTAACAAAATTCCGCAAAATGTGCTTTCAAACTT
AAAAGACGAATATTTAAATACCATAAAAACATTTATTGAACGTCCTGATT
TGTTAAAATGGAATTATCTAACTCAAGTGTTTACTTTACTTCCTAAATTG
ATCAAACAAAATAAAAAACATTTAGTTATTAAAATTTTACAATTGTGTTT
CCATTTGCTTCCAAAAAAAAGTTTTTACTTAAGTGAACATTTGGTGTTGG
GTTTAAGTAATTTGTTCTCTGCCAAGTCTTATGAACAAAAACTTTATAAT
AAATTTGCTAAATTATTTAATTTTGATTTCAAAAATCAAAATTATAAAAC
TAGTTTAATAAATTTCATACTAAAGAATAGCGTATATCTTTTTCGGTTTC
CTTCTGAAATCATCCAAGAAACAACCAATATGAAGTTAGCAATTGCAGAT
TTTGAAACTTTAACAGTAGGAAAGGCTGATTTTAAAGAATATGAAATTTT
GACTTCAGAAGTAACTGCAAAAGCTATTTGTGAACTTTATAAAAATCAAA
AATTACAAAATAATAAAAATTTGAAAAATGAATTCCTAAAATTTTAT
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protein sequence of SMED30018840-orf-1

>SMED30018840-orf-1 ID=SMED30018840-orf-1|Name=SMED30018840-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=188bp
MTYDKNQFQATVLLNDALNVLYEASLTYQNNHLTGKEIFRISFKFFEERC
DFDINKIAISNFCQFLLNSNKIYTESSNASDKTNFKKSKKVTYKMFEMND
NVNYIKKSFQHKIMSSINDGITFLRKKIGLGTKYIMCHERKFCLIHLLKI
IDLSHIENLIYLVDLSKDCEHEFDNISGEFQTKFHTQ*
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protein sequence of SMED30018840-orf-2

>SMED30018840-orf-2 ID=SMED30018840-orf-2|Name=SMED30018840-orf-2|organism=Schmidtea mediterranea sexual|type=polypeptide|length=215bp
MNTLPLYNIHWDCIFYKLKGKINKIPQNVLSNLKDEYLNTIKTFIERPDL
LKWNYLTQVFTLLPKLIKQNKKHLVIKILQLCFHLLPKKSFYLSEHLVLG
LSNLFSAKSYEQKLYNKFAKLFNFDFKNQNYKTSLINFILKNSVYLFRFP
SEIIQETTNMKLAIADFETLTVGKADFKEYEILTSEVTAKAICELYKNQK
LQNNKNLKNEFLKFY
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